2.1.

1
Microscopes and images
There is a range of microscopes for creating images of cells and
ultrastructure
Each microscope has different limits of magnification and
resolution.

Magnification is the ratio of image size to object size (size of

image/size of object). Resolution is the ability to distinguish
between two objects that are close together — the ability to provide detail in the image.

Light microscopes have a magnification of 1000-2000x, and a resolution of 50-200 nm. They are used for viewing
cells and tissues.
Light microscopes are cheap and easy to use and allow us to see living things, but their resolution is limited.

Scanning electron microscopes have a magnification of 50,000-500,000x, a resolution of 0.4-20 nm, and are used
for viewing the surface of cells and organelles and providing depth in three dimensional images.

Transmission electron microscopes have a magnification of 300,000-1,000,000x, a resolution of 0.05-1.0 nm, and
are used for detailing organelle ultrastructure.

Scanning electron and transmission electron microscopes have better resolution than a light microscope, which
means it is worth magnifying the image more as the image will show more detail. Scanning electron microscopes
also:
• give 3D images with depth of field
• are good for viewing surfaces

Electron microscopes are large and very expensive. They require trained operatives
The sample must be dried out and is therefore dead. This may affect the shape of the features seen (called an
artefact).
The image is in black and white, but colours may be added later by computer graphics. These are called false
colour electron micrographs.

Laser scanning confocal microscopes have a magnification of 1000-2000x, a resolution of 50-200 nm, and are
used to produce three dimensional images with good depth selection.

Laser scanning confocal microscopes can also see living things and have the advantage that they can focus at a
specific depth so the image is not confused by other components that are not in focus. It relies on a computer to
piece together all the information from the dots of light created by the lasers. This means that the image is an
interpretation rather than a real-life image.

Preparation of Microscope Slides

To view a specimen under a microscope it must be on a slide, a slip of thin glass called a cover slip is placed on
top of the specimen. You can prepare a slide 2 ways: dry mount or wet mount.
● Dry Mount: used with a thick specimen when you need light to be passed through, you place your
specimen on the slide and place a cover slip on top
● Wet Mount: Pipette a small drop of water onto the slide, then using tweezers place specimen on top of
slide, then place coverslip on top of specimen slowly at an angle so no air bubbles form, once slip is in
position you can add a stain to the side of the slip and put a bit of paper towel on the opposite side and the
stain will get drawn in.
Staining
Most cell components are colourless and hard to see. Staining is the application of coloured stains to the tissue or
cells. Staining:
1 makes objects visible in light microscopes
2 increases contrast so that the object can be seen more clearly
3 is often specific to certain tissues or organelles. For example, acetic orcein stains chromosomes dark red, eosin
stains cytoplasm, Sudan red stains lipids, and iodine in potassium iodide solution stains the cellulose in plant cell
walls yellow and starch granules blue/black
In an electron microscope, the stains are heavy metals or similar atoms that reflect or absorb the electrons.

Using a Stage Graticule to Calibrate an Eyepiece

Line up the eyepiece and stage micrometre, for example if each division on the micrometre is 0.1mm (1000
micrometres) long corresponds to 40 eyepiece graticule divisions, therefore 1000/40= 25 micrometres, repeat this
process every time you change magnification.

Cells
Cells are the basic unit of living organisms. All eukaryotic cells share a similar basic structure containing
membrane-bound organelles. Each organelle, whether membrane-bound or not, has its own function within the
cell.

Cell ultrastructure
The ultrastructure of a cell is the detail you can see using an electron microscope.
Organelle Structure Function Photomicrograph
Nucleus A large organelle surrounded by a nuclear The nuclear envelope separates the contents of
envelope (double membrane), which the nucleus from the rest of the cell. The pores
contains many pores called nuclear pores. contain the large DNA in the nucleus but allows
The nucleolus doesn’t have a membrane, it mRNA to leave. Nucleus contains the organism’s
contains RNA. genome and controls the cells operations.
Rough endoplasmic System of membranes, containing fluid-filled RER is an intracellular transport system; the
reticulum (RER) cavities (cisternae). Coated in ribosomes. cisternae form channels for transporting
substances around cell. Provides a large SA for
ribosomes for protein synthesis.

Smooth endoplasmic System of membranes, containing fluid-filled SER contains enzymes that catalyse reactions
reticulum (SER) cavities (cisternae). Is not coated in with lipid metabolism such as synthesis of
ribosomes. cholesterol.

Golgi Apparatus Consists of a stack of membrane-bound Proteins and modified by adding carbohydrates or
flattened sacs. Secretory vesicles bring lipids and repackaged into vesicles.
materials to and from Golgi apparatus.

Mitochondria Surrounded by a double membrane with a Site of ATP production during aerobic respiration,
fluid-filled space between them, inner they are self-replicating so more can be made if
membrane tightly folded unto cristae. Inner the demand for energy increases. They are
part of mitochondrion is a fluid-filled matric. abundant in cells where more metabolic activity
2-5 micrometres long. takes place such as muscle cells
Plasma Membrane Membrane found on the surface of animal Regulates movement of substances in and out of
cells and just inside the cell wall of plant cell. Also, contains receptor molecules on it when
cells/prokaryotic cells. Made of many lipids responds to chemicals such as hormones.
and proteins.
Ribosomes Small spherical organelles 20nm in Ribosomes bound to exterior of RER are mainly
diameter, made or rRNA, made in nucleolus for synthesising proteins that will be exported out
as two separate subunits which pass of cell. The ribosomes free in cytoplasm are
through nuclear envelope then combine, primarily the site of proteins that will be used in the
some remain in cytoplasm and attach to the cell.
endoplasmic reticulum.
Centrioles Consists of two bundles of microtubules Before a cell divides spindles forms from the
(all animal and lower perpendicular to each other. The centrioles and pull chromosomes to poles of cells.
plant cells) microtubules are made of tubulin protein As well centrioles are involved in the formation of
 subunits and are arranged to form a cilia.
cylinder.
ANIM
AL

Lysosomes Small bags formed from the Golgi, each Lysosomes can keep powerful hydrolytic enzymes
surrounded by a single membrane. Contains separate from the rest of the cell, lysosomes can
digestive enzymes. Abundant in phagocytic engulf old cell organelles and foreign matter.
cells (white blood cells) that can digest
invading pathogens.
Cell Wall The cell wall is on the outside of the plasma Cell wall is strong and can prevent plant cells from
membrane, made from bundles of cellulose bursting when turgid (swollen). It provides strength
fibres. Made of cellulose(plants), and support and maintains cell shape. It also
chitin(fungi) and peptidoglycan(bacteria). maintains the shape f the whole plant,

Chloroplasts Large organelles, 4-10 micrometres long. Chloroplasts are site of photosynthesis, the first
Only found in plant cells and Protoctista. stage, when light energy is trapped by chlorophyll
Surrounded by a double membrane, inner and used to make ATP occurs in grana. Second
membrane is continuous with stacks of stage then hydrogen reduced to carbon dioxide
PLAN

flattened membrane sacs called thylakoids using energy from ATP to make carbohydrates
T

containing chlorophyll, each stack called a occurs in the stroma.

granum. Chloroplasts contain loops of DNA
and starch grains.
Large Permanent Surrounded by a membrane called Filled with water and solutes, maintains cell
Vacuole tonoplast, contains fluid. stability and turgidity. Helpful in non-woody plants
to maintain water levels.

Cilia Protrusions from the cell and are Epithelial cells lining your airways have lots of cilia
surrounded by the cell surface membrane, that sweep mucus, they also act as receptors to
each contains microtubules and are forms detect signals from its immediate environment
from centrioles.

Flagellum Flagella on eukaryotic cells are like cilia but The microtubules contract to make the flagella
longer. They stick out from the cell surface move. They are used like outboard motoes to
and are surrounded by the plasma propel cells forward, like when a sperm cells
membrane, they are like cilia where they swims.
contain two microtubules in the entre and
nine pairs around the edge.

The organelles in a cell work together to achieve the overall function of that cell. Many of the organelles are
involved in the production and secretion of proteins. The sequence of events always follows the same course:
1 mRNA leaves the nucleus via the nuclear pores.
2 It is used by the ribosomes on the rough endoplasmic reticulum to construct a protein.
3 The protein travels in a vesicle to the Golgi apparatus.
4 The vesicle is moved by the cytoskeleton, possibly using tiny protein motors that ‘walk’ along the microtubules
using them as a track.
5 The Golgi apparatus modifies the protein (often adding a carbohydrate group) and repackages it into a vesicle.
6 This vesicle is moved to the cell-surface (plasma) membrane.
7 The vesicle fuses with the membrane to release the protein from the cell (exocytosis)

Prokaryotic and eukaryotic cells

There are two types of cells: prokaryote and eukaryote.

Animal vs. Plant Cell

Cytoskeleton
The cytoskeleton is a network of protein structures within the cytoplasm, consisting of:
● Microfilaments that are made of subunits of actin, rod-like with 7 nm diameter.
● Intermediate filaments that are about 10 nm in diameter.
● Microtubules that are the largest at 18-30 nm in diameter, made of tubulin subunits forming straight
cylinder shapes.
● Cytoskeletal motor proteins: myosins, kinesins and dyneins are all molecular motors. They are also
enzymes and have a site that binds to and allows the hydrolysis of ATP as their energy store.
The cytoskeleton allows for the movement of chromosomes in DNA replication, as well as maintaining/changing
the shape of the cell. The cytoskeleton also allows for the movement of organelles and the cell as a whole.
Test:

Section 1: Microscopes and Imaging

1. Define magnification and resolution in the context of microscopy. How are these two parameters
important in microscopy?
2. Compare and contrast light microscopes, scanning electron microscopes, and transmission electron
microscopes in terms of magnification, resolution, and application.
3. Explain why electron microscopes have better resolution than light microscopes.
4. Discuss the limitations and advantages of laser scanning confocal microscopes in comparison to
other types of microscopes.
5. What are the challenges associated with using electron microscopes, and how do they differ from
light microscopes?
6. Explain the process of preparing microscope slides using both dry mount and wet mount methods.
7. Describe the purpose of staining in microscopy and provide examples of different stains and their
applications.
8. How does a laser scanning confocal microscope differ from other microscopes in terms of image
interpretation?

Section 2: Cell Structure and Organelles

9. Define the term "cell ultrastructure." How is it observed, and why is it important?
10. Provide a detailed description of the structure and function of the nucleus in a eukaryotic cell.
11. Differentiate between rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER)
in terms of structure and function.
12. Explain the role of the Golgi apparatus in the cell, including the process of protein modification and
packaging.
13. Discuss the structure and function of mitochondria in eukaryotic cells.
14. Describe the composition and functions of the plasma membrane.
15. Explain the role of ribosomes in protein synthesis, differentiating between those bound to the
endoplasmic reticulum and free in the cytoplasm.
16. What is the function of centrioles, and in which types of cells are they found?
17. Discuss the role of lysosomes in cells, emphasizing their digestive functions.
18. Compare and contrast the cell walls of plant cells, fungal cells, and bacterial cells.
19. Explain the structure and function of chloroplasts, including the process they are involved in.
20. Define the function of the large permanent vacuole in plant cells and its role in maintaining cell
stability.

Section 3: Cell Movement and Cytoskeleton

21. Describe the components of the cytoskeleton, including microfilaments, intermediate filaments, and
microtubules.
22. Explain the roles of cytoskeletal motor proteins (myosins, kinesins, and dyneins) in cell movement
and transport.
23. Discuss how the cytoskeleton facilitates DNA replication and the maintenance of cell shape.
24. Examine the importance of the cytoskeleton in the movement of organelles and the cell as a whole.